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Detailed information for vg1123837414:

Variant ID: vg1123837414 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23837414
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAATTTCTGACTCAGATTCACCATGAGCCATGAAGCAAAAATCAGAGATGTACTCTTCCTTGTCCTTATCTTCATCACTTTTAATATCACCATTGCTTGC[C/A]
GGTTCAAAAGCAGCATAGACTTGATTTAGCACCTTCTTGAGAGCCTCCTTGGATCTTCTTCCCTTGAATGTTGTAACGGGCTTGTTGTCCTTGGTCTTGA

Reverse complement sequence

TCAAGACCAAGGACAACAAGCCCGTTACAACATTCAAGGGAAGAAGATCCAAGGAGGCTCTCAAGAAGGTGCTAAATCAAGTCTATGCTGCTTTTGAACC[G/T]
GCAAGCAATGGTGATATTAAAAGTGATGAAGATAAGGACAAGGAAGAGTACATCTCTGATTTTTGCTTCATGGCTCATGGTGAATCTGAGTCAGAAATTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.50%	0.60%	2.73%	40.10%	NA
All Indica	2759	37.60%	0.80%	3.66%	57.92%	NA
All Japonica	1512	89.70%	0.30%	1.39%	8.66%	NA
Aus	269	45.00%	1.50%	1.86%	51.67%	NA
Indica I	595	38.70%	0.30%	0.84%	60.17%	NA
Indica II	465	21.70%	0.90%	4.73%	72.69%	NA
Indica III	913	40.00%	0.90%	5.70%	53.45%	NA
Indica Intermediate	786	43.50%	1.00%	2.80%	52.67%	NA
Temperate Japonica	767	95.20%	0.30%	1.17%	3.39%	NA
Tropical Japonica	504	86.10%	0.20%	0.99%	12.70%	NA
Japonica Intermediate	241	79.70%	0.40%	2.90%	17.01%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	71.10%	0.00%	1.11%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123837414	C -> A	LOC_Os11g39960-LOC_Os11g39990	intergenic_region ; MODIFIER	silent_mutation	Average:25.465; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg1123837414	C -> DEL	N	N	silent_mutation	Average:25.465; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123837414	NA	4.92E-07	mr1411	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1123837414	NA	2.69E-06	mr1560	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1123837414	NA	3.88E-08	mr1181_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251